MICROBIAL TAXONOMY

Agus Indra Adhiputra, I Kt.

PPDS-1 MIKROBIOLOGI KLINIK
FK UNUD/ RSUP SANGLAH DENPASAR
Pembimbing: Dr. dr. Ida Sri Iswari, Sp.MK, M.Kes
 INTRODUCTION

 Taxon  Greek: Taxon = arrangement.

 Taxonomy : The science of classifying living beings.

NOMENCLATUR
E

CLASSIFICATIO IDENTIFICATIO
N N
Bailey & Scott’s Diagnostic Microbiology Fourteenth Edition. Elsevier; 2017.
Marjojie Kelly Cowan, Kathleen Park Talaro in Microbiology: A System Approach Second edition. Mc Graw Hill: 2009.
Jawetz, Melnick & Adelberg’s Medical Microbiology 27th edition. Mc Graw Hill: 2016.
 HISTORY

DOMAIN
KINGDOM
PHYLUM
CLASS

Carl
Carl von
von Linné
Linné
ORDER
(1701-1778)
(1701-1778)
FAMILY
• A hierarchical classification system GENUS
• The system of binomial nomenclature.
SPECIES
Patricia M.Tille in Bailey & Scott’s Diagnostic Microbiology Fourteenth Edition. Elsevier; 2017.
https://www.britannica.com/biography/Carolus-Linnaeus
 FROM PAST to PRESENT

1758 1866 1969 1977

Linnaeus Haeckel Whittaker Woese G. E. Fox

2 KINGDOMS 3 KINGDOMS 5 KINGDOMS 3 DOMAIN

Plantae Protista Monera Bacteria
Animalia Plantae Protista Archaea
Animalia Fungi Eukarya
Plantae
Black, J.G. Black L.J. Microbiology Principles and Explorations 9th edition. Wiley: 2015. Animalia
Marjojie Kelly Cowan, Kathleen Park
Talaro in Microbiology: A System
Approach Second edition. Mc Graw
Hill: 2009.
Marjojie Kelly Cowan, Kathleen Park Talaro in Microbiology: A System Approach Second edition. Mc Graw Hill: 2009.
Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil: 2008.
 CLASSIFICATION - Polyphasic Taxonomy

Phenetic Phenotypic characteristic.

Phylogenetic
Evolutionary relationship.

Genotypic Genotypic similarity.

Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil: 2008.

 CLASSIFICATION – Numerical Taxonomy

The grouping by numerical methods of taxonomic units into taxa on the basis of their characteristics state.

Properties of organism  numerical form (characteristics; > 50)  process in computer.

Include many different kinds of data: morphological, biochemical, and physiological.

Organism a = number of characters coded as present  

B (1) for both organisms. SSM =
1 0 b & c = numbers of characteristics differing
between the 2 organisms.
1 a b SJ =
Organism A c = number of characters absent (0) in both
0 c d organisms.

Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil; 2008.

 CLASSIFICATION – Numerical Taxonomy
Dendogram

Similarity Matrix Clusters/Phenons

Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil; 2008.

Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil; 2008.
 NOMENCLATURE

 Naming of microorganisms according to established rules and guidelines set forth in the International Code of
Nomenclature of Bacteria (ICNB) or the Bacteriological Code (BC).
 Binomial nomenclature Latin or Greek derivation.
 Genus (Capitalized), species (lowercase) italics in print or underlined when handwritten.
 Genus May be abbreviated but not species. E.g: Staphyloccous aureus  S. aureus.
 If not in Latin or Greek derivation word, will be revised to have Latin endings. E.g. Giardia lamblia  derived from
French person.

Bailey & Scott’s Diagnostic Microbiology Fourteenth Edition. Elsevier; 2017

Marjojie Kelly Cowan, Kathleen Park Talaro in Microbiology: A System Approach Second edition. Mc Graw Hill: 2009.
 IDENTIFICATION

Phenotypic Morphology Resistance Profiles

Staining Characteristics Antigenic properties

Environmental Subcellular properties

Nutrition Chemotaxonomic

Genotypic DNA base composition ratio

Nucleic acid (DNA & RNA)base sequence characteristics

Bailey & Scott’s Diagnostic Microbiology Fourteenth Edition. Elsevier; 2017
Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil; 2008.
Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil; 2008.
Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil; 2008.
Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil; 2008.
 Bergey’s Manual of Systematic Bacteriology

Vol. 1 The Archaea, & the Deeply Branching &

Phototrophic Bacteria

Vol. 2 The Proteobacteria

Vol. 3 The Low G + C Gram-Positive Bacteria

Vol. 4 The High G + C Gram-Positive Bacteria

David
David Bergey
Bergey
(1701-1778)
(1701-1778)
The Planctomycetes, Spirochates,
Vol. 5 Fibrobacteres, Bacteroidetes, Fusobacteria,
Chlamydiae, Acidobacteria, Verrumicrobia,
and Dictyoglomus
Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil; 2008.
Marjojie Kelly Cowan, Kathleen Park Talaro in Microbiology: A System Approach Second edition. Mc Graw Hill: 2009.
 VIRAL TAXONOMY

 Classified by the International Committee on the Taxonomy

of Viruses (ICTV) into numerous families, based primarily on
genome structure, replication strategy, morphology, and genetic
relatedness.

Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil; 2008.

 DNA
VIRUSES

ENVELOPE
NAKED
D

Double- Double- Single-

stranded Stranded Stranded

Icosahedral Complex Icosahedral Icosahedral

HERPES HEPADNA POX PAPOVA PARVO

ADENO
 RNA
VIRUSES

Double-
Single-Stranded
Stranded

(+) stranded (-) stranded Naked

Naked Enveloped Enveloped *REO

*PICORNA *CALICI *TOGA *FLAVI BUNYA ORTHOMYXO

CORONA RETRO PARAMYXO RHABDO

ARENA FILO

Note: * = icosahedral
 FUNGI
TAXONOMY

Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil; 2008.

 PROTIST
TAXONOMY

Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil; 2008.

 PROTIST
TAXONOMY

Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil; 2008.

 KEY POINTS

 Taxonomy is the science used to classify living organisms.

 3 primary functions: classifying, naming (nomenclature), and identifying.
 The major taxa groups: Domain, Kingdom, Phylum or Division, Class, Order, Family, Genus, and Species.
 The 3 Domains are: Bacteria, Eukarya, Archaea.
 Classification: Polyphasic taxonomy and Numerical taxonomy.
 Nomenclature: Binomial (Genus and species).
 Identification: Phenotypic and Genotypic.
 Bergey’s Manual of Systematic Bacteriology gives the accepted system of prokaryotic taxonomy.

Prescott, Harley, & Klein’s Microbiology 7th edition. McGrawHil; 2008.

Marjojie Kelly Cowan, Kathleen Park Talaro in Microbiology: A System Approach Second edition. Mc Graw Hill: 2009.
 THANK YOU

We are One Family

of
Hominoidea
Thank you
 INTRODUCTION

 Nomenclature is  the assignment of scientific names to the various taxonomic categories and individual
organisms.
 Classification is a method for organizing microorganisms into groups or taxa based on similar morphologic,
physiologic, and genetic traits.
 Identification is  the process of discovering and recording the traits or organisms so that they may be
recognized or named and placed in an overall taxonomic scheme.

Patricia M.Tille in Bailey & Scott’s Diagnostic Microbiology Fourteenth Edition. Elsevier; 2017.
Marjojie Kelly Cowan, Kathleen Park Talaro in Microbiology: A System Approach Second edition. Mc Graw Hill: 2009.
Jawetz, Melnick & Adelberg’s Medical Microbiology 27th edition. Mc Graw Hill: 2016.
 CLASSIFICATION – Family

 A group of organism that may contain multiple genera and consists of organism with a common attribute.
 Suffix –aceae.

Bailey & Scott’s Diagnostic Microbiology Fourteenth Edition. Elsevier; 2017.

 CLASSIFICATION - Genus

 Plural: Genera.
 Based on various genetic and phenotypic characteristics among species.
 Establishing microorganism’s relatedness in higher taxa beyond the genus level is difficult.

Bailey & Scott’s Diagnostic Microbiology Fourteenth Edition. Elsevier; 2017.

 CLASSIFICATION - Species

 Abbreviation: sp.  singular; spp.  plural.

 Share common physiologic and genetic features, differ notably from other microbial species.
 Subspecies  subgroups within a species.

Bailey & Scott’s Diagnostic Microbiology Fourteenth Edition. Elsevier; 2017.

 IDENTIFICATION

Morphology Physiology Phage typing

Staining Biochemistry Sequence of bases in tRNA

Growth Genetics Protein profiles

Nutrition Serology

Black, J.G. Black L.J. Microbiology Principles and Explorations 9th edition. Wiley: 2015.
 Identification Criteria and Characteristics for
Microbial Classification
Phenotypic

Criteria Characteristics
Macroscopic as observed with the unaided eye.
morphology e.g. texture, & pigmentation of bacterial colonies.
Microscopic as observed with aid of microscopic magnification.
morphology e.g. size, shape, intracellular inclusions, cellular appendages, & cell arrangement
Staining The characteristics to reproducibly stain color with the application of specific dyes and reagents.
characteristics e.g. gram positive (purple), gram negative (red).
Environmental The characteristics to grow at various temperatures, in the presence of oxygen and other gases, at
requirements various pH levels, or in the presence of other ions and salts, such as NaCl.
Resistance profiles The inherent resistance to specific antibiotics, heavy metals, or toxins.

Bailey & Scott’s Diagnostic Microbiology Fourteenth Edition. Elsevier; 2017.

 Identification Criteria and Characteristics for
Microbial Classification

Phenotypic

Criteria Characteristics
Nutritional The characteristics to utilize various carbon and nitrogen sources as nutritional substrates when
requirements grown under specific environmental conditions.
Antigenic properties The characteristics to established profiles by various serologic and immunologic methods to
determine relatedness among various microbial groups.
Subcellular properties The molecular constituents of the cell that are typical of a particular taxon, or organism group.
e.g. cell wall components, components of the cell membrane, and enzymatic content of the
microbial cell.
Chemotaxonomic The chemical constituents of the cell.
properties e.g. structure of teichoic acids, fatty acid analysis, and protein profiles.

Bailey & Scott’s Diagnostic Microbiology Fourteenth Edition. Elsevier; 2017.

 Identification Criteria and Characteristics for
Microbial Classification

Genotypic

Criteria Characteristics
DNA base composition Using G + C content.
ratio e.g. an organism with a G  + C content of 50% is not closely related to an organism with a G
+ C content of 25%.
DNA & RNA base The degree of similarity in the sequences may be a measure of the degree of organism
sequence characteristics relatedness, specifically, the ribosomal RNA (rRNA) sequences that remain stable in
comparison to the genome as a whole.

Bailey & Scott’s Diagnostic Microbiology Fourteenth Edition. Elsevier; 2017.

 Role of Taxonomy in Diagnostic Microbiology

 Established and maintains records of key characteristics of clinically relevant microorganisms.

 Facilitates communication among technologists, microbiologists, physicians, and scientists by assigning universal names
to clinically relevant microorganisms. This is essential for:
 Establishing an association of particular diseases or syndromes with specific microorganisms.
 Epidemiology and tracking outbreaks.
 Accumulating knowledge regarding the management and outcome diseases associated with specific microorganisms.
 Establishing patterns of resistance to antimicrobial agents and recognition of changing microbial resistance patterns.
 Understanding the mechanisms of antimicrobial resistance and detecting new resistance mechanisms exhibited by
microorganisms.
 Recognizing new and emerging pathogenic microorganisms.
 Recognizing changes in the types of infections or diseases caused by characteristic microorganisms.
 Revising and updating available technologies for the development of new methods to optimize the detection and identification of
infectious agents and the detection of resistance to anti-infective agents (microbial, viral, fungal, and parasitic).
 Developing new anti-infective therapies (microbial, viral, fungal, and parasitic).
Bailey & Scott’s Diagnostic Microbiology Fourteenth Edition. Elsevier; 2017.
 Role of Taxonomy in Diagnostic Microbiology

Records of key characteristics Antimicrobial resistance mechanisms

Universal name for microorganisms Recognize new pathogenic microorganisms

Association of disease to microorganism Recognize change of type of infection

Epidemiology Updating available technologies

Management and outcome Develops new antimicrobial

Antimicrobial resistance patterns

Bailey & Scott’s Diagnostic Microbiology Fourteenth Edition. Elsevier; 2017.

CLASSIFICATION OF VIRUSES

 Viruses, acellular infectious agents that share only a few characteristics with living organisms are not
included in any of the 5 kingdoms. Viruses are classified by their nucleic acids, chemical composition, and
morphology.